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- PDB-8xa2: Penton capsomer of the VZV B-Capsid -

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Basic information

Entry
Database: PDB / ID: 8xa2
TitlePenton capsomer of the VZV B-Capsid
Components
  • Major capsid protein
  • Tri1
  • Tri2A
  • Tri2B
KeywordsVIRUS / VZV / capsid structures
Function / homologyT=16 icosahedral viral capsid / Herpesvirus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpes virus major capsid protein / host cell nucleus / structural molecule activity / Major capsid protein
Function and homology information
Biological speciesHuman alphaherpesvirus 3 (Varicella-zoster virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsNan, W. / Lei, C. / Xiangxi, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Hlife / Year: 2024
Title: Insights into varicella-zoster virus assembly from the B- and C-capsid at near-atomic resolution structures
Authors: Cao, L. / Wang, N. / Lv, Z. / Chen, W. / Chen, Z. / Song, L. / Sha, X. / Wang, G. / Hu, Y. / Lian, X. / Cui, G. / Fan, J. / Quan, Y. / Liu, H. / Hou, H. / Wang, X.
History
DepositionDec 1, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major capsid protein
C: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
R: Tri2A
V: Tri2B
Z: Tri1


Theoretical massNumber of molelcules
Total (without water)850,5468
Polymers850,5468
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Major capsid protein / MCP


Mass: 152365.312 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Gene: ORF40, MCP, ORF 40, HHV3_E_SVETAgp42, HHV3_gp42, HHV3gp42
Production host: Homo sapiens (human) / References: UniProt: Q6QCL5
#2: Protein Tri2A


Mass: 27729.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Production host: Homo sapiens (human)
#3: Protein Tri2B


Mass: 28721.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Production host: Homo sapiens (human)
#4: Protein Tri1


Mass: 32268.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human alphaherpesvirus 3 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Details of virusEmpty: NO / Enveloped: YES / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7.3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 267174 / Symmetry type: POINT

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